Abstract
We present an implementation of an in vitro signal recorder based on DNA assembly and strand displacement. The signal recorder implements a stack data structure in which both data as well as operators are represented by single stranded DNA “bricks”. The stack grows by adding push and write bricks and shrinks in last-in-first-out manner by adding pop and read bricks. We report the design of the signal recorder and its mode of operations and give experimental results from capillary electrophoresis as well as transmission electron microscopy that demonstrate the capability of the device to store and later release several successive signals. We conclude by discussing potential future improvements of our current results.
H. Fellermann and A. Lopiccolo—Contributed equally to this work.
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References
Seeman, N.C.: DNA in a material world. Nature 421(6921), 427–431 (2003)
Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Proc. Nat. Acad. Sci. USA 107(12), 5393–5398 (2010)
Stojanović, M.N., Stefanović, D.: Deoxyribozyme-Based Half-Adder. J. Am. Chem. Soc. 125(22), 6673–6676 (2003)
Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314(5805), 1585–1588 (2006)
Cardelli, L.: Strand algebras for DNA computing. Nat. Comput. 10, 407–428 (2011)
Chen, Y., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G.: Programmable chemical controllers made from DNA. Nat. Nano. 8(10), 755–762 (2013)
Qian, L., Winfree, E.: A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface 8(62), 1281–1297 (2011)
Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034), 1196–201 (2011)
Li, W., Zhang, F., Yan, H., Liu, Y.: DNA based arithmetic function: a half adder based on DNA strand displacement. Nanoscale 8(6), 3775–3784 (2016)
Liu, H., Wang, J., Song, S., Fan, C., Gothelf, K.V.: A DNA-based system for selecting and displaying the combined result of two input variables. Nature Comm. 6, 10089 (2015)
MacDonald, J., Li, Y., Sutovic, M., Lederman, H., Pendri, K., Lu, W., Andrews, B.L., Stefanovic, D., Stojanovic, M.N.: Medium scale integration of molecular logic gates in an automaton. Nano Lett. 6(11), 2598–2603 (2006)
Qian, L., Soloveichik, D., Winfree, E.: Efficient turing-universal computation with DNA polymers. In: Sakakibara, Y., Mi, Y. (eds.) DNA 16 2010. LNCS, vol. 6518, pp. 123–140. Springer, Heidelberg (2011)
Terrazas, G., Gheorghe, M., Kendall, G., Krasnogor, N.: Evolving tiles for automated self-assembly design. In: IEEE Congress on Evolutionary Computation, CEC 2007, pp. 2001–2008 (2007)
Siepmann, P., Martin, C.P., Vancea, I., Moriarty, P.J., Krasnogor, N.: A genetic algorithm approach to probing the evolution of self-organized nanostructured systems. Nano Lett. 7(7), 1985–1990 (2007)
Woolley, R.A.J., Stirling, J., Radocea, A., Krasnogor, N., Moriarty, P.: Automated probe microscopy via evolutionary optimization at the atomic scale. Appl. Phys. Lett. 98(25), 253104 (2011)
Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., Hofacker, I.L.: ViennaRNA Package 2.0. Algorithms. Mol. Biol. 6(1), 26 (2011)
Doye, J.P.K., Ouldridge, T.E., Louis, A.A., Romano, F., Šulc, P., Matek, C., Snodin, B.E.K., Rovigatti, L., Schreck, J.S., Harrison, R.M., Smith, W.P.J.: Coarse-graining DNA for simulations of DNA nanotechnology. Phys. Chem. Chem. Phys. 15(47), 20395 (2013)
Hadorn, M., Bnzli, E., Fellermann, H., Eggenberger Hotz, P., Hanczyc, M.: Specific and reversible DNA-directed self-assembly of emulsion droplets. Proc. Nat. Acad. Sci. USA 109(47) (2012)
Fellermann, H., Cardelli, L.: Programmable chemistry in DNA addressable bioreactors. R. Soc. Interface 11(99), 20130987 (2014)
Acknowledgments
This work has been supported by EPSRC grant agreements no EP/J004111/1, EP/J004111/2, EP/L001489/1, EP/L001489/2. We thank Chien-yi Chang, Christoph Flamm, Alessandro Ceccarelli, Omer Markovitch, and Ben Shirt-Ediss for helpful discussions.
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Fellermann, H., Lopiccolo, A., Kozyra, J., Krasnogor, N. (2016). In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement. In: Amos, M., CONDON, A. (eds) Unconventional Computation and Natural Computation. UCNC 2016. Lecture Notes in Computer Science(), vol 9726. Springer, Cham. https://doi.org/10.1007/978-3-319-41312-9_8
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